[gmx-users] struggles with cyclic peptides
jalemkul at vt.edu
Mon Sep 14 13:03:29 CEST 2015
On 9/14/15 6:58 AM, Nikhil wrote:
> Hi Justin,
> So your saying working with Gromacs for cyclic peptide is hopeless using
> available methods?
I don't see a way to do it.
> i tried all terminals
> in .tdb file removing C ,O and H from -COOH so that only O will add up
> and before that removing O from the pdb ,i tired that but ends up with
> lots of errors.
> i found in archives same issues as connection establishing with C-N but
> extra atoms at each terminals ..!
Right, in principle, you can generate "normal" termini, delete the unnecessary
atoms, renumber *everything* in the topology from 1, and write in the bonded
interactions (bonds, angles, dihedrals) and it will work. That's a lot of
effort and is very error prone.
One possibility, since you want to use CHARMM, is to use CHARMM-GUI to set
things up. It is quite straightforward and supports cyclic peptides. Our
latest version of the server provides all GROMACS topology and input files for
doing the run.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
More information about the gromacs.org_gmx-users